User: angrypigeon

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angrypigeon120
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Posts by angrypigeon

<prev • 70 results • page 1 of 7 • next >
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Comment: C: Convert mouse amino acid location to genomic location
... This works great! But how did you find the protein id instead of the gene id? ...
written 1 day ago by angrypigeon120
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Comment: C: Convert mouse amino acid location to genomic location
... This doesn't seem to work for me either. I am trying to get the coordinates for the mouse `DNMT3a R878H` mutation in the question like this: https://rest.ensembl.org/vep/human/hgvs/ENSMUSG00000020661:p.Arg878His?content-type=application/json But this will not return anything. ...
written 1 day ago by angrypigeon120
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Comment: C: Convert mouse amino acid location to genomic location
... Thanks Pierre, I did have a look at this but it is unclear how to perform such an analysis for mouse. It looks like the Ensembl API might be able to do it as illustrated [here][1], but how to switch from human to mouse is not clear to me. [1]: https://rest.ensembl.org/documentation/info/assembly ...
written 1 day ago by angrypigeon120
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Convert mouse amino acid location to genomic location
... I have amino acid positions for a number of mouse mutations, for example `DNMT3a R878H`. Is there a way to convert this to a genome coordinate such as` chr12:12345`? The Ensembl Rest API seems to be capable of such a task, and when I make a call for a human change it works as shown here: https ...
genome gene written 1 day ago by angrypigeon120
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Separate Genome into Tiers
... I've seen the genome separated into tiers based on functionality; something like Tier I: coding and Tier III: non-coding, non-repeating, non-conserved. Is there a way to match these classifications up with actual genomic locations? I am working specifically with mouse at the moment but it would be g ...
genome written 8 months ago by angrypigeon120
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Comment: C: How to get orthologous sequence
... This actually works pretty well. I grabbed a targeted region of sequence from UCSC with something like this: wget -O - http://genome.ucsc.edu/cgi-bin/das/hg38/dna?segment=%s:%s,%s >> locs\n' % (chrom, low, high) Then used this in UCSC BLAT to find the orthologous region within mouse. (Th ...
written 8 months ago by angrypigeon120
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Comment: C: How to get orthologous sequence
... This is what I don't know how to do. I can see how the mouse gene can be accessed, but then how to target a particular hotspot within that region and identify its coordinates? ...
written 8 months ago by angrypigeon120
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Comment: C: How to get orthologous sequence
... This is an interesting resource, but I'm still not quite sure how this would help me target a particular sequence. The reference you point to seems to do a nice job of identifying the entire gene region, but how would I target a particular hotspot within the given gene? ...
written 8 months ago by angrypigeon120
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How to get orthologous sequence
... Is there a nice way to get orthologous sequence of a particular gene locus? As an example of what I'm trying to do: Say I have the gene CTNNB1 that is commonly mutated in humans at chr3:41266124. Now, I would like to convert this location to the mouse genome and get the surrounding gDNA sequence. ...
genome gene written 8 months ago by angrypigeon120 • updated 8 months ago by lieven.sterck5.4k
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Get gene names from ensembl ID or gene region
... I have some RNASeq data that has fpkm values labeled with genome positions like `chr7 52823165 52830546` Ensembl IDs like `ENSMUST00000143813` and gene symbols like `0610005C13Rik`. Is there a good programmatic way in python to get gene names from any of this data so I can match up the fpkm values w ...
ensembl rna-seq python written 9 months ago by angrypigeon120 • updated 9 months ago by Alex Reynolds28k

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